@@ -1,5 +1,5 @@

 Package: bsseq

-Version: 1.23.0

+Version: 1.23.1

 Encoding: UTF-8

 Title: Analyze, manage and store bisulfite sequencing data

 Description: A collection of tools for analyzing and visualizing bisulfite

@@ -11,10 +11,10 @@ Depends:

     R (>= 3.5),

     methods,

     BiocGenerics,

-    GenomicRanges (>= 1.29.14),

-    SummarizedExperiment (>= 1.9.18)

+    GenomicRanges (>= 1.33.6),

+    SummarizedExperiment (>= 1.17.4)

 Imports:

-    IRanges (>= 2.11.16),

+    IRanges (>= 2.21.6),

     GenomeInfoDb,

     scales,

     stats,

@@ -23,7 +23,7 @@ Imports:

     locfit,

     gtools,

     data.table (>= 1.11.8),

-    S4Vectors (>= 0.23.11),

+    S4Vectors (>= 0.25.14),

     R.utils (>= 2.0.0),

     DelayedMatrixStats (>= 1.5.2),

     permute,

@@ -22,10 +22,12 @@

 # Internal methods -------------------------------------------------------------

-# NOTE: Combine the new parallel slots with those of the parent class. Make

-#       sure to put the new parallel slots *first*.

+# NOTE: Combine the new "vertical slots" with those of the parent class. Make

+#       sure to put the new vertical slots **first**. See R/bindROWS.R file in

+#       the S4Vectors package for what slots should or should not be considered

+#       "vertical".

 setMethod(

-    "parallelSlotNames",

+    "vertical_slot_names",

     "FWGRanges",

     function(x) {

         c(GenomicRanges:::extraColumnSlotNames(x), "seqnames", "ranges",

@@ -35,7 +35,7 @@ setValidity2("FWIRanges", .valid.FWIRanges)

 # Internal methods -------------------------------------------------------------

-setMethod("parallelSlotNames", "FWIRanges",

+setMethod("vertical_slot_names", "FWIRanges",

           function(x) c("start", "NAMES", callNextMethod())

 )

@@ -53,7 +53,7 @@ setMethod("end", "FWIRanges", function(x) {

 setMethod("names", "FWIRanges", function(x) x@NAMES)

-setMethod("parallelSlotNames", "FWIRanges",

+setMethod("vertical_slot_names", "FWIRanges",

           function(x) c("start", "NAMES", callNextMethod())

 )